Background:The FabI inhibitor CG400549 is a promising new anti-staphylococcal drug candidate with recently validated human efficacy. Results: We revealed the molecular determinants conferring S. aureus FabI selectivity to rationally design a compound with an improved antibacterial activity spectrum.
Conclusion:The 4-pyridone PT166 represents a critical step toward Gram-negative and mycobacterial coverage. Significance: We provide an approach to expand the spectrum of antimicrobial activity.
A critical goal of lead compound selection and optimization is to maximize target engagement whilst minimizing off-target binding. Since target engagement is a function of both the thermodynamics and kinetics of drug-target interactions, it follows that the structures of both the ground states and transition states on the binding reaction coordinate are needed to rationally modulate the lifetime of the drug-target complex. Previously, we predicted the structure of the rate-limiting transition state that controlled the time-dependent inhibition of the enoyl-ACP reductase InhA. This led to the discovery of a triazole-containing diphenyl ether with an increased residence time on InhA due to transition state destabilization rather than ground state stabilization. In the present work, we have evaluated the inhibition of InhA by 14 triazole-based diphenyl ethers and used a combination of enzyme kinetics and X-ray crystallography to generate a structure-kinetic relationship (SKR) for time-dependent binding. We show that the triazole motif slows the rate of formation for the final drug-target complex by up to three orders of magnitude. In addition, we identify a novel inhibitor with a residence time on InhA of 220 min which is 3.5-fold longer than that of the INH-NAD adduct formed by the tuberculosis drug, isoniazid. This study provides a clear example in which the lifetime of the drug-target complex is controlled by interactions in the transition state for inhibitor binding rather than the ground state of the enzyme-inhibitor complex, and demonstrates the important role that on-rates can play in drug-target residence time.
The aquaglyceroporin 7 (AQP7) facilitates permeation of glycerol through cell membranes and is crucial for lipid metabolism in humans. Glycerol efflux in human adipocytes is controlled by translocation of AQP7 to the plasma membrane upon hormone stimulation.Here we present two X-ray structures of human AQP7 at 1.9 and 2.2 Å resolution. The structures combined with molecular dynamics simulations suggest that AQP7 is a channel selective for glycerol and that glycerol may hamper water permeation through the channel. Moreover, the high resolution of the structures facilitated a detailed analysis of the orientation of glycerol in the pore, disclosing unusual positions of the hydroxyl groups. The data suggest that glycerol is conducted by a partly rotating movement through the channel. These observations provide a framework for understanding the basis of glycerol efflux and selectivity in aquaglyceroporins and pave the way for future design of AQP7 inhibitors.
The
enoyl-acyl carrier protein (ACP) reductase (ENR) is a key enzyme
within the bacterial fatty-acid synthesis pathway. It has been demonstrated
that small-molecule inhibitors carrying the diphenylether (DPE) scaffold
bear a great potential for the development of highly specific and
effective drugs against this enzyme class. Interestingly, different
substitution patterns of the DPE scaffold have been shown to lead
to varying effects on the kinetic and thermodynamic behavior toward
ENRs from different organisms. Here, we investigated the effect of
a 4′-pyridone substituent in the context of the slow tight-binding
inhibitor SKTS1 on the inhibition of the Staphylococcus aureus enoyl-ACP-reductase saFabI and the closely related isoenzyme from Mycobacterium tuberculosis, InhA, and explored a new interaction
site of DPE inhibitors within the substrate-binding pocket. Using
high-resolution crystal structures of both complexes in combination
with molecular dynamics (MD) simulations, kinetic measurements, and
quantum mechanical (QM) calculations, we provide evidence that the
4′-pyridone substituent adopts different tautomeric forms when
bound to the two ENRs. We furthermore elucidate the structural determinants
leading to significant differences in the residence time of SKTS1
on both enzymes.
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